Welcome

• Peter Steinbach (HZDR)

A short introduction to the sprint

Transparent, reproducible, and adaptable data analysis with Snakemake

• Johannes Köster (Universitätsklinikum Essen)

The Snakemake workflow management system is a tool to create transparent, reproducible and adaptable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment. With over 600,000 downloads and over 1600 citations (on average >7 per week), Snakemake is one of the most widely used systems for reproducible data analysis.

An Introduction to Efficient and Scalable Pipeline Management with Nextflow

• Marcel Ribeiro-Dantas (Seqera Labs)

Nextflow is an open-source workflow orchestration tool for data-intensive pipelines. It has rapidly become an industry standard, enabling scalable and reproducible scientific workflows. Nextflow has a vibrant community with thousands of bioinformaticians as part of the nf-core project, which provides ready-to-use pipelines, ready-to-plug-in modules, and sub-workflows. Nextflow simplifies the implementation and deployment of complex workflows across almost all compute infrastructures - from HPC job schedulers to all of the main cloud providers. It has built-in support for software packaging tools such as Docker, Podman, Singularity, conda, automatically managing workflow toolchains and facilitating scalable and reproducible scientific workflows. In this talk I will introduce Nextflow and nf-core, explaining how the workflow manager works, the community tools available to streamline development, and how to get started building your own pipelines. Write your pipeline once, and run it anywhere

Introduction to CWL and Workflowhub

• Michael R. Crusoe

Team Spotlight: P11 / DESY HH

• Helena Tabermann

Team Spotlight: FAXTOR / ALBA

• Alessandra Patera

Team Spotlight: KARA / KIT

• Yaroslav Zharov

Team Spotlight: Michal & Mikhail

• Michal Smid

Team Pairing

• Peter Steinbach (HZDR)